getCoordGeneSets {esetVis} | R Documentation

## extract coordinates gene sets

### Description

extract coordinates gene sets

### Usage

    getCoordGeneSets(dataPlotGenes, geneSets, esetUsed, geneSetsVar = list())

### Arguments

`dataPlotGenes` | data.frame with two columns 'X' and 'Y' with coordinates for the genes
`geneSets` | geneSets list of gene sets, e.g. gene pathways, output from the 'getGeneSets' function in MLP the genes IDs must correspond to the sampleNames in the eset
`esetUsed` | expressionSet (or SummarizedExperiment) object with data
`geneSetsVar` | variable of the featureData used to match the genes contained in geneSets, most probably ENTREZID, if NULL the featureNames of the eSet are used

### Value

data.frame with two columns 'X' and 'Y' with coordinates for the gene sets

### Author(s)

Laure Cougnaud

Laure Cougnaud

[Package esetVis version 1.12.0 Index]